× Didn't find what you were looking for? Ask a question
Top Posters
Since Sunday
5
o
5
4
m
4
b
4
x
4
a
4
l
4
t
4
S
4
m
3
s
3
New Topic  
someone here someone here
wrote...
Posts: 8
Rep: 0 0
5 years ago
Hi!
I was wondering if anyone out there would know why I should go with an UPGMA guide tree based method as opposed to a neighborjoining (NJ) guide tree based method.
From what I can tell, UPGMA creates rooted trees and NJ creates unrooted trees. But why would I choose one over the other?
Read 709 times
6 Replies

Related Topics

Replies
wrote...
5 years ago
They use different algorithms to build the from a distance matrix. You can check the details of those algorithms for the Wikipedia:

http://en.wikipedia.org/wiki/UPGMA
http://en.wikipedia.org/wiki/Neighbor_joining

The most important practical issues: UPGMA provides rooted tree as a result, while NJ unrooted, and you have to take care proper rooting the NJ tree afterward.

Also, UPGMA is regarded as an unreliable method, so I would prefer to use NJ.

Bootstrapping is a re-sampling method used in phylogenetics to estimate the reliability of individual branching points of a tree:

http://en.wikipedia.org/wiki/Bootstrapping_(statistics)

As a first approach, bootstrap values tell you how much you can "trust" a branch on a phylogenetic tree. The bigger the better. Values over 0.9 (90%) are usually OK. (But that depends on your data and research question too.) Values below 0.6 (60%) are usually no-go.
Source  Online
wrote...
5 years ago
The Unweighted Pair-Group Method  with Arithmetic Averaging (UPGMA) algorithm (left) assumes equal rates of evolution, so that branch tips come out equal. The Neighbor-Joining (NJ) (right) algorithm allows for unequal rates of evolution, so that branch lengths are proportional to amount of change. If rates on different branches are not markedly unequal, the branching orders produced by the two methods will not differ, as in this example with Carnivora.



Alternative UPGMA & NJ phenetic analyses of Panda relationships
someone h. Author
wrote...
5 years ago
Thanks guys!
One further question - why would a rooted or unrooted tree or assuming equal or unequal rates of evolution be beneficial for one scenario versus another?
wrote...
Valued Member
Educator
5 years ago


The first sentence explains the benefit of one over the other
someone h. Author
wrote...
5 years ago
Thank you very much for your help! Appreciate all the insight. Makes perfect sense when someone explains it like that.
wrote...
Valued Member
Educator
5 years ago
Our pleasure Smiling Face with Open Mouth

Reviewing your next inquiry now
New Topic      
Explore
Post your homework questions and get free online help from our incredible volunteers
  1119 People Browsing
Related Images
  
 2145
  
 272
  
 442
Your Opinion
Which industry do you think artificial intelligence (AI) will impact the most?
Votes: 308